Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with bishydroxamic acid inhibitor
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (CD2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VNR
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- R5G, K, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 353 | 43% helix, 14% strand | A7YT55 |
| B | HDAC6 protein | protein | 355 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- R5G · N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.59 | 0.78 | 41 | R5G |
| 2 | 122 | 0.52 | 0.81 | 21 | empty |
| 3 | 202 | 0.50 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VNR · Crystal Structure of Danio rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A7YT55
- Elsewhere: RCSB PDB 6VNR · PDBe 6VNR · UniProt A7YT55
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